Last Updated: January 2009
© 2009 CFSPH
page 2 of 27
Antigenic shift and drift in influenza A viruses
Influenza A viruses change frequently. Strains evolveas they accumulate point mutations during virusreplication; this process is sometimes called ‘antigenicdrift’.
A more abrupt change can occur during geneticreassortment. Reassortment is possible whenever twodifferent influenza viruses infect a cell simultaneously;when the new viruses (the ‘progeny’) are assembled, theymay contain some genes from one parent virus and somegenes from the other.
Reassortment between differentstrains results in the periodic emergence of novel strains.Reassortment between subtypes can result in theemergence of a new subtype. Reassortment can also occurbetween avian, swine, equine, canine and humaninfluenza A viruses. This type of reassortment can resultin a ‘hybrid’ virus with, for example, both avian andhuman influenza virus proteins.An abrupt change in the subtypes found in a hostspecies is called an ‘antigenic shift.’ Antigenic shifts canresult from three mechanisms: 1) genetic reassortmentbetween subtypes, 2) the direct transfer of a whole virusfrom one host species into another, or 3) the re-emergenceof a virus that was found previously in a species but is nolonger in circulation.
For example, human viruses cancontinue to circulate in pigs and could re-emerge into thehuman population.
Antigenic drift and antigenic shiftsresult in the periodic emergence of novel influenzaviruses. By evading the immune response, these virusescan cause influenza epidemics and pandemics.
Avian influenza viruses
Avian influenza viruses are found in a wide variety of domesticated and wild birds.
They are also isolatedoccasionally from mammals including humans.
Waterfowl (order Anseriformes) and shorebirds(order Charadriiformes) seem to be the natural reservoirsfor the type A influenza viruses, and carry all of theknown subtypes.
The predominant subtypes inwild ducks change periodically.
Most, though not all,infections in wild waterfowl and shorebirds areasymptomatic.
Poultry can be infected by a wide variety of subtypes;some of these viruses cause avian influenza. Avianinfluenza viruses are classified as either high pathogenicityavian influenza (HPAI) viruses or low pathogenicity avianinfluenza (LPAI) viruses, based on the genetic features of the virus and the severity of disease in poultry.
To date,only subtypes that contained H5 or H7 have caused HPAI;subtypes that contained other hemagglutinins have beenfound only in the LPAI form.
H5 and H7 LPAI virusesalso exist, and can evolve into high pathogenicitystrains.
From 1993 to 2000, LPAI subtypes containingH1 to H7 and H9 to H11 were isolated from live birdmarkets in the northeastern U.S.
Limited information is available on the subtypesfound in other species of birds. Subtypes that have beenfound in ratites include H3N2, H4N2, H4N6, H5N1,H5N2, H5N9, H7N1, H7N3, H9N2, H10N4 andH10N7.
Isolates from cage birds usually containH3 or H4; however, infections with high pathogenicitysubtypes containing H7 or H5 can also occur.
Swine influenza viruses
Swine influenza viruses are found mainly in pigs, butthey have also been found in other species includinghumans.
There is less antigenic drift in swineinfluenza viruses than in human influenza A viruses.
The most common subtypes currently found in pigs areH1N1, H1N2 and H3N2 ;however, the situation iscomplex, as two or more viruses of each subtype arecirculating in swine populations.
Recently, H3N1influenza viruses have also been isolated from pigs in theU.S. and Korea,
and H2N3 influenza viruses weredetected in pigs in the U.S.
One H1N1 virus circulating in the U.S. is the‘classical H1N1 swine influenza virus. This virus, the firstinfluenza virus known to have infected pigs, was firstfound in swine populations in 1918.
An ‘avian-like’ H1N1 virus circulates in European and U.S.pigs.
This virus seems to be an avian influenza virusthat was transmitted whole to pigs.
It has, in somelocations, replaced the classical H1N1 virus.
Adifferent ‘avian-like’ H1N1 virus is co-circulating withthe classical H1N1 virus in pigs in Asia.
In addition,H1N1 reassortant viruses consisting of classical swineinfluenza virus genes and a human PB1 polymerase genehave been found in pigs in Canada.
A wholly humanlineage H1N1 virus was recently reported from pigs inChina.
This virus, which was responsible for anoutbreak of acute respiratory illness in a herd inGuangdong, has been designatedA/Swine/Guangdong/96/06 (H1N1).
In North America, H3N2 viruses first emerged inpigs in the U.S. Midwest.
The viruses found in theU.S. are triple reassortants.
They containhemagglutinin and neuraminidase proteins from a humaninfluenza virus, and internal proteins from the classicalswine influenza virus, an avian influenza virus and ahuman influenza virus.
New triple reassortant H3N2viruses have recently been found in Canada.
Theseviruses resemble the H3N2 viruses isolated in the U.S.,but contain a different neuraminidase gene from a humaninfluenza virus.
They have been isolated from pigs,turkeys and a Canadian swine farmer.
H3N2 viruses arealso found in Europe and Asia, but these viruses seem tobe the result of reassortment between a human H3N2virus, circulating there in pigs since the 1970s, and theH1N1 ‘avian-like’ virus.
The European H3N2 virusescontain human H3 and N2 proteins, and internal proteinsfrom the avian virus.
The H1N2 virus in the U.S. is a reassortant of theclassical H1N1 swine influenza virus and the triplereassortant H3N2 virus circulating in the U.S.
SomeH1N2 viruses in Canadian pigs contain neuraminidaseand hemagglutinin genes from two different human